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--- how_to:web:quantitationresults [2015/07/22 15:59]
193.48.0.3
+++ how_to:web:quantitationresults [2016/07/06 16:56] (current)
193.48.0.3
@@ Line 2: / Line 2: @@
 ====== Quantitation Summary ======
-{{ :how_to:web:quanti_summary.png?direct |}}
 This panel is a summary of your experimental design, listing your biological groups, their samples and their technical replicates.
 It also provides the "Profile Analysis" tool you need to launch in order to get Ratio informations and data to be exported.
+{{ :how_to:web:dse_quant_results_summary.png?nolink |}}
+----
 ====== Proteins ======
-{{ :how_to:web:quanti_proteines.png?direct |}}
+{{ :how_to:web:dse_quant_results_proteins.png?nolink |}}
-This panel show all the data about the quantified proteins. **In order to see the ratio values, you have to launch the Profile Analysis from the Summary Panel.**
+This panel show all the data about the quantified proteins. By default, proteins are grouped, but you can undo it by clicking the icon circled in green in the previous screenshot. The view will then be:
-Double-clicking a Protein will open its summary panel :
+{{ :how_to:web:dse_quant_results_proteins_ungrouped.png?nolink |}}
-{{ :how_to:web:protein_summary.png?direct |}}
+This grid is also provided a filter tool, that you can use as follows:
-On this panel, you get an insight of all quantified peptides for this protein. You can click on "Raw XIC" to access the XIC viewer of one Peptide .
+{{ :how_to:web:dse_quant_results_proteins_filters.png?nolink |}}
-{{ :how_to:web:quanti_peptide_xic.png?direct |}}
+Double-clicking a Protein will open the //Protein details// panel :
+=== Protein details panel ===
+{{ :how_to:web:protein_quanti_details.png?direct |}}
+On this panel, you get an insight of all quantified peptides for this protein (double click on the peptide in the 'Quantified Peptides' table or expand directly the peptide panel).
+{{ :how_to:web:peptide_quanti_details.png?direct |}}
+ You can click on the eye icon (circled in green) to access the Speclight viewer of this Peptide .
+TODO: insert link to Speclight doc
+----
 ====== Peptides ======
-{{ :how_to:web:quanti_peptides.png?direct |}}
+{{ :how_to:web:dse_quant_results_peptides.png?nolink |}}
+This is the list of all quantified peptides.
+  * Click on a peptide to see its Master Quant Peptide Ions in the dedicated table below.
+  * Double-click on a peptide to open the panel for the feature corresponding to this peptide (see [[#LC-MS Features |LC-MS Features]]).
-This is the list of all quantified peptides. Double-clicking on one of them will open the panel for the feature corresponding to this peptide (see below).
+Note that the peptide grid has got a filter tool too.
 ====== LC-MS Maps ======
-This panel offers two tabs to give you informations about the Lc-Ms maps of the experiment.
+This panel offers two tabs to give you information about the LC-Ms maps of the experiment.
-Click on one or many raw files to display their Lc-Ms map features.
-{{ :how_to:web:quanti_lcms_maps.png?direct |}}
+==== Map alignments ====
-The "Map alignment" tab shows a chart describing the map alignment correction performed by Proline for the analysis.
+** IMPORTANT: it is crucial to visit this graphics to manually control the processed map alignments.
+A bad alignment (showing many curve trends, or too large time deltas) will lead to quantitation errors.**
+If you have the feeling that the alignment needs improvement, re-run the quantitation, tunning the //Alignment Computation// part of the //LFQ Params// tab (see [[how_to:web:createquantitation|how to create a quantitation]]).
-{{ :how_to:web:quanti_map_align.png?direct |}}
+{{ :how_to:web:dse_quant_results_maps_alignment.png?nolink |}}
+On this chart, you can see all the delta time of each LC-MS map against the reference LC-MS map. The reference map is the one specified in the title of the chart. It corresponds to the x axis.
+==== LC-MS maps 2D viewer ====
+Click on one or many raw files to display their LC-Ms map features.
+{{ :how_to:web:dse_quant_results_maps_2d.png?nolink |}}
+----
 ====== LC-MS Features ======
-This panel lists all the features detected and processed by Proline. By clicking one of them, you can see the corresponding XIC on the right-side panel.
+This panel lists all the features detected and processed by Proline.\\
+Click a **master feature** to see:
+- the corresponding XIC on the right-side panel
+- the corresponding features in each file in the bottom grid (first tab)
+- the corresponding master quant. peptide ion in the bottom gris (second tab).
-{{ :how_to:web:quanti_lcms.png?direct |}}
+You can double click an entry in the bottom grid to open a dedicated tab (feature/peptide ion details).
+{{ :how_to:web:dse_quant_results_features.png?nolink |}}
+----
 ====== LC-MS Peaks ======
 All the peaks are listed here, independently from the features they've been gathered to.
-Click on a Lc-Ms Map name to list all its peaks. By clicking on a peak you can see its XIC charts in the "XIC Viewer" at the bottom of the table, or you can double-click it to open the Xic Viewer in a new tab.
-{{ :how_to:web:quanti_peaks.png?direct |}}
+Click on a LC-MS Map to list all its peaks in the center grid. Note that this grid is provided a filtering tool.
+Click on a peak (center grid) to see its feature and XIC charts in the bottom panel.
+You can alternatively double-click a peak to open the XIC Viewer in a new tab.
+{{ :how_to:web:dse_quant_results_peaks.png?nolink |}}
+----
 ====== Quantitation Stats ======
-This tab offers many panel to help you vizualise statistics about your quantitation.
+==== Post Processing ====
-The first one is a volcano chart of your Proteins based on their -Log10 T-Test P-Value over Log2 Ratio.
+{{ :how_to:web:dse_launch_post_processing.png?350|}}
+**In order to see the statistics on the ratios, you have to launch the Post Processing (previously called //Profile Analysis//).** Launch it from the //Summary// tab toolbar, or from the quantitation node (in project tree) context menu.
+You can see the //Post Processing// configuration window below.\\
+See [[prolineconcepts:lcmsquantitationadvancedconfig| more details on the post-processing parameters]].\\
+Launch the post processing by clicking //Run//. You can watch the task progression in the //Tasks// window. You will also be notified when the task is done. You can then watch the results in the //Quantitation Stats// tab.
+{{ :how_to:web:dse_post_processing.png?nolink |}}
+==== Quantitation Statistics ====
+This tab offers many panel to help you visualize statistics about your quantitation.
+=== Proteins volcano plot ===
+The first panel is a volcano chart of your Proteins based on their -Log10 T-Test P-Value over Log2 Ratio.
+{{ :how_to:web:dse_quant_results_protein_volcano.png?nolink |}}
 The Left grid shows a list of all the proteins, and if they are in the actual boudaries of the selection/exclusion tool.
-The "AC Filters" let you select a color (by clicking on it) and enter an Accession Number (or a part of it) to highlight matching proteins on the chart).
+Hover a dot to see information on the protein.\\
+Click on it to open its [[#Protein details panel|protein details panel]].
+The //AC Filters// let you select a color (by clicking on it) and enter an Accession Number (or a part of it) to highlight matching proteins on the chart). In this example, all proteins containing "HUMAN" in their accession number are colored in orange. By defaults, dots are light blue.
+The //Log2 Fold Change// (of the ratios) and //P-Value// fields let you define new boundaries for the protein selection/exclusion. It's show on the chart with black lines and gray points to show excluded proteins.
-The "Ratio" et "P-Value" let you define new boundaries for the protein selection / exclusion. It's show on the chart with black lines and gray points to show excluded proteins.
+{{ :how_to:web:dse_quant_results_protein_volcano_filtered.png?nolink |}}
-{{ :how_to:web:quanti_volcano_prot.png?direct |}}
+Select a zone with the mouse cursor to zoom on it.
+Use the icon at the top-right of the volcano plot to export it at several picture formats.
-The second tab offers the same volcano chart for peptides, and you can highlight them with a sequence or ptm definition
+=== Peptides volcano plot ===
-{{ :how_to:web:quanti_volcano_pep.png?direct |}}
+The second tab offers the same volcano chart and options for peptides. Instead of accession number, you can color the dots according to their sequence or PTM definition.
+{{ :how_to:web:dse_quant_results_peptide_volcano.png?nolink |}}

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